package edu.vt.sdm.tcga.data;

import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.List;
import java.util.Properties;

//Don't use complicated data structure! Improved the efficiency of data mining tasks.
public class ExpressionLevel2Model{
	public class Row {
		private int __index;
		
		public int getIndex() {
			return __index;
		}
		public void setIndex(int index) {
			__index = index;
		}
		public Row(int i) {
			setIndex(i);
		}
	}
	
	private static ExpressionLevel2Model __instance = null;

	// The following fields used to store data queried from the database.
	private ArrayList<String> __SampleList = new ArrayList<String>();
	private ArrayList<String> __GeneList = new ArrayList<String>();
	private double[][] __GeneData;

	// The following fields used to store processed data.
	private ArrayList<String> __SampleOfInterestList = new ArrayList<String>(); // Get from user or
																// logic
	private ArrayList<String> __GeneOfInterestList = new ArrayList<String>(); // Get from user or
															// logic
	private double[][] __GeneDataOfInterest; // Generated from __GeneData
	private List<Row> __GeneDataOfDisplay = new ArrayList<Row>();

	private double __MaxSignal = 0;
	private double __MinSignal = 0;
	
	//Database related
	private final static String urlTCGA = "jdbc:postgresql://8.15.251.49:5432/TCGA";

	public static synchronized ExpressionLevel2Model getInstance() {
		if (__instance != null) {
			return __instance;
		}
		__instance = new ExpressionLevel2Model();
		__instance.setTestData();
//		__instance.LoadData();
		return __instance;
	}

	public void setSampleList(ArrayList<String> __SampleList) {
		this.__SampleList = __SampleList;
	}

	public ArrayList<String> getSampleList() {
		return __SampleList;
	}

	public void setGeneList(ArrayList<String> __GeneList) {
		this.__GeneList = __GeneList;
	}

	public ArrayList<String> getGeneList() {
		return __GeneList;
	}

	public void setGeneData(double[][] __GeneData) {
		this.__GeneData = __GeneData;
	}

	public double[][] getGeneData() {
		return __GeneData;
	}

	public void setSampleOfInterestList(ArrayList<String> __SampleOfInterestList) {
		this.__SampleOfInterestList = __SampleOfInterestList;
	}

	public ArrayList<String> getSampleOfInterestList() {
		return __SampleOfInterestList;
	}

	public void setGeneOfInterestList(ArrayList<String> __GeneOfInterestList) {
		this.__GeneOfInterestList = __GeneOfInterestList;
	}

	public ArrayList<String> getGeneOfInterestList() {
		return __GeneOfInterestList;
	}

	public void setGeneDataOfInterest(double[][] __GeneDataOfInterest) {
		this.__GeneDataOfInterest = __GeneDataOfInterest;
	}

	public double[][] getGeneDataOfInterest() {
		return __GeneDataOfInterest;
	}

	public void setMaxSignal(double __MaxSignal) {
		this.__MaxSignal = __MaxSignal;
	}

	public double getMaxSignal() {
		return __MaxSignal;
	}

	public void setMinSignal(double __MinSignal) {
		this.__MinSignal = __MinSignal;
	}

	public double getMinSignal() {
		return __MinSignal;
	}
	
	private void LoadData() {
    	// Database context
    	Connection conn = null;
    	Statement st = null;
    	ResultSet rs = null;
    	String strTemplate = "select gene,value from expression_level_2 where patientnumber in (1,3,6,7,9);";
    	
    	String strSQL = null;
    	String strTemp = null;

    	Properties props = new Properties();
    	props.setProperty("user","eric");
    	props.setProperty("password","");
    	try {
    		//Prepare for the query SQL statement.
    		strSQL = strTemplate;
    		
				Class.forName("org.postgresql.Driver");
    		
    		//Get database connection and create query statement.
			conn = DriverManager.getConnection(urlTCGA, props);
			st = conn.createStatement();
			rs = st.executeQuery(strSQL);

			while (rs.next()) {
				strTemp = rs.getString(1);
				strTemp = rs.getString(1);
			}

	        //Database close
			rs.close();
			st.close();
			conn.close();	
			
			//Service close //do nothing
		} catch (SQLException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		} catch (ClassNotFoundException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		} finally {
		}
    	
        return;		
	}

	public void setTestData() {
		setMaxSignal(14.3415995631444);
		setMinSignal(3.09392270966443);
		__SampleOfInterestList.add("TCGA-02-0001-01C-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0003-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0006-01B-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0007-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0009-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0010-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0011-01B-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0014-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0021-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0024-01B-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0027-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0028-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0033-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0034-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0037-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0038-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0043-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0046-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0047-01A-01R-0177-01");
		__SampleOfInterestList.add("TCGA-02-0052-01A-01R-0177-01");
		__GeneOfInterestList.add("1007_s_at");
		__GeneOfInterestList.add("1053_at");
		__GeneOfInterestList.add("117_at");
		__GeneOfInterestList.add("121_at");
		__GeneOfInterestList.add("1255_g_at");
		__GeneOfInterestList.add("1294_at");
		__GeneOfInterestList.add("1316_at");
		__GeneOfInterestList.add("1320_at");
		__GeneOfInterestList.add("1405_i_at");
		__GeneOfInterestList.add("1431_at");
		__GeneOfInterestList.add("1438_at");
		__GeneOfInterestList.add("1487_at");
		__GeneOfInterestList.add("1494_f_at");
		__GeneOfInterestList.add("1598_g_at");
		__GeneOfInterestList.add("160020_at");
		__GeneOfInterestList.add("1729_at");
		__GeneOfInterestList.add("177_at");
		__GeneOfInterestList.add("1773_at");
		__GeneOfInterestList.add("179_at");
		__GeneOfInterestList.add("1861_at");
		__GeneOfInterestList.add("200000_s_at");
		__GeneOfInterestList.add("200001_at");
		__GeneOfInterestList.add("200002_at");
		__GeneOfInterestList.add("200003_s_at");
		__GeneOfInterestList.add("200004_at");
		__GeneOfInterestList.add("200005_at");
		__GeneOfInterestList.add("200006_at");
		__GeneOfInterestList.add("200007_at");
		__GeneOfInterestList.add("200008_s_at");
		__GeneOfInterestList.add("200009_at");
		__GeneOfInterestList.add("200010_at");
		__GeneOfInterestList.add("200011_s_at");
		__GeneOfInterestList.add("200012_x_at");
		__GeneOfInterestList.add("200013_at");
		__GeneOfInterestList.add("200014_s_at");
		__GeneOfInterestList.add("200015_s_at");
		__GeneOfInterestList.add("200016_x_at");
		__GeneOfInterestList.add("200017_at");
		__GeneOfInterestList.add("200018_at");
		__GeneOfInterestList.add("200019_s_at");
		__GeneOfInterestList.add("200020_at");
		__GeneOfInterestList.add("200021_at");
		__GeneOfInterestList.add("200022_at");
		__GeneOfInterestList.add("200023_s_at");
		__GeneOfInterestList.add("200024_at");
		__GeneOfInterestList.add("200025_s_at");
		__GeneOfInterestList.add("200026_at");
		__GeneOfInterestList.add("200027_at");
		__GeneOfInterestList.add("200028_s_at");
		__GeneOfInterestList.add("200029_at");
		__GeneOfInterestList.add("200030_s_at");
		__GeneOfInterestList.add("200031_s_at");
		__GeneOfInterestList.add("200032_s_at");
		__GeneOfInterestList.add("200033_at");
		__GeneOfInterestList.add("200034_s_at");
		__GeneOfInterestList.add("200035_at");
		__GeneOfInterestList.add("200036_s_at");
		__GeneOfInterestList.add("200037_s_at");
		__GeneOfInterestList.add("200038_s_at");
		__GeneOfInterestList.add("200039_s_at");
		__GeneOfInterestList.add("200040_at");
		__GeneOfInterestList.add("200041_s_at");
		__GeneOfInterestList.add("200042_at");
		__GeneOfInterestList.add("200043_at");
		__GeneOfInterestList.add("200044_at");
		__GeneOfInterestList.add("200045_at");
		__GeneOfInterestList.add("200046_at");
		__GeneOfInterestList.add("200047_s_at");
		__GeneOfInterestList.add("200048_s_at");
		__GeneOfInterestList.add("200049_at");
		__GeneOfInterestList.add("200050_at");
		__GeneOfInterestList.add("200051_at");
		__GeneOfInterestList.add("200052_s_at");
		__GeneOfInterestList.add("200053_at");
		__GeneOfInterestList.add("200054_at");
		__GeneOfInterestList.add("200055_at");
		__GeneOfInterestList.add("200056_s_at");
		__GeneOfInterestList.add("200057_s_at");
		__GeneOfInterestList.add("200058_s_at");
		__GeneOfInterestList.add("200059_s_at");
		__GeneOfInterestList.add("200060_s_at");
		__GeneOfInterestList.add("200061_s_at");
		__GeneOfInterestList.add("200062_s_at");
		__GeneOfInterestList.add("200063_s_at");
		__GeneOfInterestList.add("200064_at");
		__GeneOfInterestList.add("200065_s_at");
		__GeneOfInterestList.add("200066_at");
		__GeneOfInterestList.add("200067_x_at");
		__GeneOfInterestList.add("200068_s_at");
		__GeneOfInterestList.add("200069_at");
		__GeneOfInterestList.add("200070_at");
		__GeneOfInterestList.add("200071_at");
		__GeneOfInterestList.add("200072_s_at");
		__GeneOfInterestList.add("200073_s_at");
		__GeneOfInterestList.add("200074_s_at");
		__GeneOfInterestList.add("200075_s_at");
		__GeneOfInterestList.add("200076_s_at");
		__GeneOfInterestList.add("200077_s_at");
		__GeneOfInterestList.add("200078_s_at");
		__GeneOfInterestList.add("200079_s_at");

		int k = 0;
		__GeneDataOfInterest = new double[__GeneOfInterestList.size()][__SampleOfInterestList.size()];
		for (int i = 0; i < __GeneOfInterestList.size(); i++) {
			for (int j = 0; j < __SampleOfInterestList.size(); j++) {
				__GeneDataOfInterest[i][j] = TestGeneData[k];
				k++;
			}
		}
	}

	public List<Row> getGeneDataOfDisplay() {
		__GeneDataOfDisplay.clear();
		for (int i = 0; i < __GeneOfInterestList.size(); i++) {
			__GeneDataOfDisplay.add(new Row(i));
		}		
		return __GeneDataOfDisplay;
	}
	
	public String getTableCell(int inRow, int inCol) {
		if(inCol == 0) {
			return __GeneOfInterestList.get(inRow);
		} else {
			return String.valueOf(__GeneDataOfInterest[inRow][inCol]);
		}
	}

	private static int __ColumnDisplayIndex = 0; //old display
	public String getTableCell(int inRow) {
		String strResult = null;
		if(__ColumnDisplayIndex == 0) {
			strResult = __GeneOfInterestList.get(inRow);
		} else {
			strResult = String.valueOf(__GeneDataOfInterest[inRow][__ColumnDisplayIndex - 1]); 
		}
		__ColumnDisplayIndex = (__ColumnDisplayIndex + 1) % (__SampleOfInterestList.size() + 1);
		return strResult;
	}

	
	private double[] TestGeneData = new double[] { 10.8852645127063,
			11.1253856768528, 11.071471876993, 10.4232353673775,
			11.4348662671957, 10.4645179708236, 11.1896571468983,
			9.76866151747375, 10.9701743683295, 7.20097630190386,
			7.72393639589946, 6.8175612707688, 7.77477138747425,
			6.98223387919965, 7.0611111469119, 6.36903691685768,
			7.6246057183646, 7.42757784566971, 4.93926485155326,
			4.83758266326816, 6.00475543079787, 4.67970336929616,
			4.27816392138251, 4.52053870320044, 4.6838819747336,
			4.19266602545432, 4.95640355676323, 6.14345680245191,
			5.85794989285798, 6.03156535642628, 5.96604309566336,
			6.24251076920928, 6.09757871079585, 5.93889452336956,
			5.69548196413071, 6.16657871206894, 3.93381919672011,
			3.51307684304196, 4.03850732250642, 3.56108242404268,
			3.72346477408275, 3.62431824785717, 3.5032971104178,
			3.54016512421965, 3.64722080301821, 6.7174721725055,
			5.72533378904837, 6.3143231759466, 7.11210675492568,
			6.66350158445185, 5.60605408258762, 6.39983675977966,
			4.68203155203589, 6.36754074763511, 4.00739153674967,
			3.8891182608739, 3.96548477113205, 4.03138464999295,
			4.09013061168903, 4.57836839185048, 4.44394327856591,
			4.86691387331035, 4.00993826412016, 4.00550671945282,
			3.95740734771564, 3.86865050066086, 3.77506926372912,
			4.31214708748021, 3.86014856775471, 3.75481523367624,
			3.85179708757396, 3.91009705661081, 4.77389676060168,
			3.95578987037924, 4.16129817427283, 3.74565960115768,
			3.98130855236454, 3.98889143555743, 3.82785196906792,
			3.81534657432293, 4.7416116031057, 3.73086827829318,
			3.75720011987961, 3.82754353769248, 3.9247406757787,
			3.74302835997035, 4.33219129834538, 3.88627046241992,
			3.80697785104297, 3.72498946144805, 4.20378025402283,
			5.77779549245914, 3.97465967263852, 4.38607095941622,
			4.48069273887843, 4.80958760587227, 4.80424072395743,
			6.16146917955784, 4.48828494789505, 5.8474856332761,
			4.92404832673322, 5.14119918331072, 4.66445740554716,
			4.64014499778209, 5.11408030294812, 5.44900005569158,
			6.14006698121186, 5.50143287063338, 4.06404383300595,
			4.09541816624232, 4.17011192650019, 4.14269119031374,
			4.00170813913365, 4.09809181835334, 4.58299055646015,
			4.37139384636776, 4.21274403333456, 8.03240795220429,
			6.81955670566676, 7.55063982809065, 9.11879885996787,
			7.44547734099773, 7.09153265927887, 7.02875473986619,
			6.32768526675277, 8.02065248522495, 6.58670695462453,
			5.52232955456414, 5.62198984616517, 6.86841102168709,
			5.4800837513206, 5.46635037065399, 5.03420107043603,
			5.20799595850885, 5.95820062944544, 7.10426550413969,
			5.86625482111959, 6.47719474353782, 6.1776179413311,
			6.17125738049577, 6.08367706354196, 5.68292793868516,
			5.07181377256708, 6.33161019148537, 5.31296778620706,
			5.35574807425226, 5.60798344930112, 4.71044063744102,
			5.87512803428788, 4.90516541340117, 4.78414166337226,
			5.25096415405276, 4.84698816618131, 4.17662295066926,
			3.94633636154968, 4.08692904718784, 3.88649557523293,
			4.16026069510183, 3.81021300886959, 3.79947281504673,
			3.81697026724471, 4.00260039493697, 5.93116283147882,
			5.6052274802648, 5.63129659586562, 5.58411151257597,
			5.3896121681669, 5.89039733852586, 5.67744448821042,
			5.82615498406323, 5.85553326163184, 6.72167185968975,
			6.98527032051186, 6.81447519969562, 6.63471069837879,
			6.89207914977818, 6.3477453740562, 7.48658208194678,
			7.17987951142106, 6.98599618765367, 9.29372336952154,
			9.67212789885575, 10.0682098283353, 10.4298124925048,
			10.2811926998118, 10.9457884233644, 10.2028379182018,
			10.5938715587499, 9.75595957011739, 10.3337603578483,
			10.2186895397791, 10.3741606105732, 9.9863480750849,
			10.6436724182812, 9.42253530894443, 10.0704600929108,
			9.90683313459283, 10.4903779064885, 11.7444828761534,
			11.7882022295234, 11.7241287652532, 11.7985104008826,
			11.7081727084926, 12.2252057116795, 11.9427916386807,
			11.2651924063045, 12.1250071742857, 12.9711894751963,
			12.8364353808661, 13.141067711097, 12.790756701164,
			13.3344421218357, 13.1976435868276, 12.9754462040137,
			13.1921432291529, 13.4848976093136, 11.5897869801141,
			11.4350010599882, 11.4518040799132, 11.7978790725413,
			11.5736392596255, 11.476037086716, 11.3119215765719,
			12.2035231775785, 11.5028470212388, 9.82656620857955,
			9.88270686343544, 9.9292301843082, 8.89930389846739,
			10.1164553584428, 10.4322105918085, 10.0424055617706,
			10.7320471661112, 10.1712333660725, 12.1453823313084,
			12.2069597573148, 12.0790700812041, 12.5155910968945,
			11.5402729476318, 12.2547786978979, 12.4545471493184,
			12.4237937417397, 12.2708602545861, 11.2833782528298,
			10.900798414193, 11.4477558059625, 12.1931773292096,
			11.4281863362968, 11.8735055572133, 11.0973642277794,
			11.8028635051206, 11.6081520400089, 9.65841921591007,
			9.06065962716642, 9.0405753509402, 9.4404555678225,
			8.64432643200242, 9.42368572953729, 9.58804577454781,
			10.5346854365215, 8.87465235129173, 11.5646051871914,
			10.7816158614795, 10.9343747991097, 11.3605093643472,
			10.6268450431505, 11.2912873741462, 11.9778285886195,
			12.1922462931685, 10.7953799577935, 11.6747981397815,
			11.3791495281384, 11.8398356866246, 11.5008920439918,
			11.7743949265148, 12.5171197166741, 11.4574820478113,
			12.0049906516435, 11.9234068906017, 10.7894570708978,
			10.2646532392822, 10.083064637123, 9.58249004692412,
			10.2106006412202, 9.8270366258946, 10.7705384871705,
			9.73860878942477, 10.1403149058056, 13.0769753960435,
			12.9082079509194, 12.7265035592311, 12.7491824346969,
			12.9287875750875, 13.1620728838223, 12.7245830110782,
			13.1900197578986, 13.1059877371209, 12.0718538695869,
			12.184328273047, 12.0588946947259, 12.1530532732867,
			11.9200449711363, 12.5019171719638, 12.1236265080492,
			12.4934597062653, 12.2258131657969, 10.3591500005361,
			10.6738672740394, 10.5194645187286, 10.8668023967977,
			10.757999534887, 10.9872427155106, 10.5899835806711,
			11.0994869688661, 10.6641221718028, 11.6481929590907,
			12.167775239647, 11.6405224108339, 11.3349305045111,
			11.8532972051947, 11.721711843786, 11.9165626410809,
			11.5063797917952, 11.7831218346817, 12.2587030928135,
			12.8135539665357, 12.680922694198, 12.7559230755357,
			12.8681540877757, 13.1635470795105, 12.733253080421,
			13.1732324129464, 12.7519126298943, 12.9223605939581,
			12.6039528288932, 12.8609879501459, 12.7739626300905,
			12.797368290509, 13.1422563100536, 12.8283561682686,
			12.8957400920727, 12.8417608965784, 12.7787150268182,
			12.5409184854498, 13.030701469335, 12.8649853930546,
			12.9005406471134, 12.8346195809056, 13.002986415959,
			13.0401596992659, 12.8170392518271, 12.4814331057715,
			12.6362325569402, 12.897654629163, 12.2331939671362,
			12.6857368593071, 12.8267408344858, 13.0531361364791,
			12.9366979440124, 12.7902651984363, 8.79383178334957,
			8.8882596483026, 8.43111400754239, 8.91018791746215,
			8.77057070026815, 9.23858061876263, 8.84929528916262,
			9.7366618731564, 9.05107505362335, 13.4701490837858,
			13.8229531846006, 13.6114934816695, 13.0037467179427,
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}
